Showing metabocard for 3-Dehydroquinate (MMDBc0029770)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:40:58 UTC
Update Date2022-08-31 17:16:49 UTC
Metabolite IDMMDBc0029770
Metabolite Identification
Common Name3-Dehydroquinate
Description3-dehydroquinate is a member of the chemical class known as Cyclitols and Derivatives. These are compounds containing a cycloalkane moiety with one hydroxyl group on each of three or more ring atoms. 3-dehydroquinate is invovled in phenylalanine, tyrosine and tryptophan biosynthesis, and the biosynthesis of secondary metabolites. Dehydroquinate is involved in the shikimate pathway. The aroB-encoded enzyme dehydroquinate synthase is the second enzyme of this pathway, and it catalyzes the cyclization of 3-deoxy-D-arabino-heptulosonate-7-phosphate in 3-dehydroquinate. The aroB-encoded enzyme dehydroquinate synthase is the second enzyme of this pathway, and it catalyzes the cyclization of 3-deoxy-D-arabino-heptulosonate-7-phosphate in 3-dehydroquinate. (PMID 17586643 ) The aroB gene encoding dehydroquinate synthase (DHQS), which is a potential antibiotic target, was identified from the plant-pathogenic bacterium Xanthomonas oryzae pv. (PMID 19052366 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f5a64742668>


  Mrv1652309042000362D          

 13 13  0  0  0  0            999 V2000
10000.1518 9999.9041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.8661 9999.4913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.151810000.7298    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.1518 9999.0784    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2909 9999.9041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7209 9997.4272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2909 9998.2528    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7208 9999.9037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.0064 9999.4913    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.0064 9998.6663    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.7208 9998.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4353 9998.6663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4353 9999.4913    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  8  9  1  0  0  0  0
  8 13  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  1 13  1  0  0  0  0
 13  4  1  1  0  0  0
  9  5  1  6  0  0  0
 11  6  2  0  0  0  0
 10  7  1  1  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f5a64742668>

HMDB0012710
     RDKit          3D
3-Dehydroquinic acid
 23 23  0  0  0  0  0  0  0  0999 V2000
   -0.8911   -2.2625    1.3574 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6389   -1.4588    0.4925 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7656   -1.2603    0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0886    0.2123    0.2879 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7864    0.5751    1.5961 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5010    0.4213   -0.0326 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2984    0.8805    0.8240 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9606    0.1065   -1.3007 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1503    0.9884   -0.6200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2529    0.7966   -0.1100 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1603    1.5459   -0.8364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6802   -0.6564   -0.1778 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9358   -0.7911    0.3729 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4820   -1.9240    0.5694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7893   -1.4098   -1.0392 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8384    1.5631    1.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9202   -0.8391   -1.6600 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3998    2.0664   -0.4705 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2626    0.6794   -1.6772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2512    1.0770    0.9624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639    1.9923   -0.2092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7135   -0.9695   -1.2553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9551   -1.3333    1.1938 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  1
  4  6  1  0
  6  7  2  0
  6  8  1  0
  4  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12  2  1  0
  3 14  1  0
  3 15  1  0
  5 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  1
 11 21  1  0
 12 22  1  6
 13 23  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f5a64742668>


  Mrv1652309042000362D          

 13 13  0  0  0  0            999 V2000
10000.1518 9999.9041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.8661 9999.4913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.151810000.7298    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.1518 9999.0784    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2909 9999.9041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7209 9997.4272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2909 9998.2528    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7208 9999.9037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.0064 9999.4913    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.0064 9998.6663    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.7208 9998.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4353 9998.6663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4353 9999.4913    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  8  9  1  0  0  0  0
  8 13  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  1 13  1  0  0  0  0
 13  4  1  1  0  0  0
  9  5  1  6  0  0  0
 11  6  2  0  0  0  0
 10  7  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029770

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@@H]1C[C@@](O)(CC(=O)[C@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O6/c8-3-1-7(13,6(11)12)2-4(9)5(3)10/h3,5,8,10,13H,1-2H2,(H,11,12)/t3-,5+,7-/m1/s1

> <INCHI_KEY>
WVMWZWGZRAXUBK-SYTVJDICSA-N

> <FORMULA>
C7H10O6

> <MOLECULAR_WEIGHT>
190.1507

> <EXACT_MASS>
190.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.45823621642952

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3R,4S)-1,3,4-trihydroxy-5-oxocyclohexane-1-carboxylic acid

> <ALOGPS_LOGP>
-2.05

> <JCHEM_LOGP>
-2.0552498786666664

> <ALOGPS_LOGS>
0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.359570129279923

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.304489138555496

> <JCHEM_PKA_STRONGEST_BASIC>
-3.272742784069651

> <JCHEM_POLAR_SURFACE_AREA>
115.06000000000002

> <JCHEM_REFRACTIVITY>
38.6974

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.02e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-dehydroquinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f5a64742668>

HMDB0012710
     RDKit          3D
3-Dehydroquinic acid
 23 23  0  0  0  0  0  0  0  0999 V2000
   -0.8911   -2.2625    1.3574 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6389   -1.4588    0.4925 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7656   -1.2603    0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0886    0.2123    0.2879 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7864    0.5751    1.5961 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5010    0.4213   -0.0326 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2984    0.8805    0.8240 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9606    0.1065   -1.3007 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1503    0.9884   -0.6200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2529    0.7966   -0.1100 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1603    1.5459   -0.8364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6802   -0.6564   -0.1778 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9358   -0.7911    0.3729 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4820   -1.9240    0.5694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7893   -1.4098   -1.0392 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8384    1.5631    1.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9202   -0.8391   -1.6600 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3998    2.0664   -0.4705 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2626    0.6794   -1.6772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2512    1.0770    0.9624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639    1.9923   -0.2092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7135   -0.9695   -1.2553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9551   -1.3333    1.1938 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  1
  4  6  1  0
  6  7  2  0
  6  8  1  0
  4  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12  2  1  0
  3 14  1  0
  3 15  1  0
  5 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  1
 11 21  1  0
 12 22  1  6
 13 23  1  0
M  END
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PDB for #<Metabolite:0x00007f5a64742668>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8666.9508666.488   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8668.2838665.717   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8666.9508668.029   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8666.9508664.946   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8661.6108666.488   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8664.2798661.864   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8661.6108663.405   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8664.2798666.487   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8662.9458665.717   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8662.9458664.177   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8664.2798663.407   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8665.6138664.177   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8665.6138665.717   0.000  0.00  0.00           C+0
CONECT    1    2    3   13                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4   13                                                            
CONECT    5    9                                                            
CONECT    6   11                                                            
CONECT    7   10                                                            
CONECT    8    9   13                                                       
CONECT    9    8   10    5                                                  
CONECT   10    9   11    7                                                  
CONECT   11   10   12    6                                                  
CONECT   12   11   13                                                       
CONECT   13    8   12    1    4                                             
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for #<Metabolite:0x00007f5a64742668>

COMPND    HMDB0012710
HETATM    1  O1  UNL     1      -0.891  -2.262   1.357  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.639  -1.459   0.492  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.766  -1.260   0.078  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.089   0.212   0.288  1.00  0.00           C  
HETATM    5  O2  UNL     1       0.786   0.575   1.596  1.00  0.00           O  
HETATM    6  C4  UNL     1       2.501   0.421  -0.033  1.00  0.00           C  
HETATM    7  O3  UNL     1       3.298   0.880   0.824  1.00  0.00           O  
HETATM    8  O4  UNL     1       2.961   0.106  -1.301  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.150   0.988  -0.620  1.00  0.00           C  
HETATM   10  C6  UNL     1      -1.253   0.797  -0.110  1.00  0.00           C  
HETATM   11  O5  UNL     1      -2.160   1.546  -0.836  1.00  0.00           O  
HETATM   12  C7  UNL     1      -1.680  -0.656  -0.178  1.00  0.00           C  
HETATM   13  O6  UNL     1      -2.936  -0.791   0.373  1.00  0.00           O  
HETATM   14  H1  UNL     1       1.482  -1.924   0.569  1.00  0.00           H  
HETATM   15  H2  UNL     1       0.789  -1.410  -1.039  1.00  0.00           H  
HETATM   16  H3  UNL     1       0.838   1.563   1.654  1.00  0.00           H  
HETATM   17  H4  UNL     1       2.920  -0.839  -1.660  1.00  0.00           H  
HETATM   18  H5  UNL     1       0.400   2.066  -0.470  1.00  0.00           H  
HETATM   19  H6  UNL     1       0.263   0.679  -1.677  1.00  0.00           H  
HETATM   20  H7  UNL     1      -1.251   1.077   0.962  1.00  0.00           H  
HETATM   21  H8  UNL     1      -2.764   1.992  -0.209  1.00  0.00           H  
HETATM   22  H9  UNL     1      -1.714  -0.969  -1.255  1.00  0.00           H  
HETATM   23  H10 UNL     1      -2.955  -1.333   1.194  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   12
CONECT    3    4   14   15
CONECT    4    5    6    9
CONECT    5   16
CONECT    6    7    7    8
CONECT    8   17
CONECT    9   10   18   19
CONECT   10   11   12   20
CONECT   11   21
CONECT   12   13   22
CONECT   13   23
END
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SMILES for #<Metabolite:0x00007f5a64742668>

O[C@@H]1C[C@@](O)(CC(=O)[C@H]1O)C(O)=O
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INCHI for #<Metabolite:0x00007f5a64742668>

InChI=1S/C7H10O6/c8-3-1-7(13,6(11)12)2-4(9)5(3)10/h3,5,8,10,13H,1-2H2,(H,11,12)/t3-,5+,7-/m1/s1
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Synonyms
ValueSource
5-Dehydroquinic acidChEBI
5-DehydroquinateKegg
3-DehydroquinateGenerator
3-Dehydroquinic acidGenerator, KEGG
Cyclohexan-1,4,5-triol-3-one-1-carboxylic acidHMDB
(1R,3R,4S)-1,3,4-Trihydroxy-5-oxocyclohexanecarboxylic acidHMDB
1,3,4-Trihydroxy-5-oxocyclohexanecarboxylic acidHMDB
Molecular FormulaC7H10O6
Average Mass190.1507
Monoisotopic Mass190.047738052
IUPAC Name(1R,3R,4S)-1,3,4-trihydroxy-5-oxocyclohexane-1-carboxylic acid
Traditional Name3-dehydroquinic acid
CAS Registry NumberNot Available
SMILES
O[C@@H]1C[C@@](O)(CC(=O)[C@H]1O)C(O)=O
InChI Identifier
InChI=1S/C7H10O6/c8-3-1-7(13,6(11)12)2-4(9)5(3)10/h3,5,8,10,13H,1-2H2,(H,11,12)/t3-,5+,7-/m1/s1
InChI KeyWVMWZWGZRAXUBK-SYTVJDICSA-N